Genome-wide identification and characterization of reference genes with different transcript abundances for Streptomyces coelicolor.
Genome-wide identification and characterization of reference genes with different transcript abundances for Streptomyces coelicolor.
复制标题
天蓝色链霉菌具有不同转录本丰度的参考基因的全基因组鉴定和表征
DOI：
10.1038/srep15840
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发表时间：
2015-11-03
影响因子：
4.6
通讯作者：
Yang K
中科院分区：
文献类型：
--
作者：
Li S;Wang W;Li X;Fan K;Yang K
在链霉菌属中缺乏可靠的参考基因(RGS)阻碍了获得转录水平的准确数据的努力。为了解决这个问题，我们的目标是在模式生物天蓝色链霉菌中鉴定可靠的RGS。通过确定在不同条件下培养的天蓝色链霉菌M145的四个时间序列转录组微阵列数据集中具有稳定转录水平的基因的交集，首次确定了包含1,471个基因的潜在RGS池。经过严格的同源性分析、干扰分析、功能分析和转录丰度分析，从1,471个基因中筛选出13个候选基因。根据实时定量逆转录聚合酶链式反应分析，SCO0710、SCO6185、SCO1544、SCO3183和SCO4758是13个候选基因中转录水平最稳定的前5个基因。进一步的分析表明，这5个基因在不同的天蓝色链霉菌以及阿维链霉菌MA-4680和棒状链霉菌NRRL 3585中也保持了稳定的转录水平，表明它们可以满足链霉菌准确数据标准化的要求。此外，本工作所采用的系统策略也可为其他微生物筛选可靠的RGS提供借鉴。
The lack of reliable reference genes (RGs) in the genus Streptomyces hampers effort to obtain the precise data of transcript levels. To address this issue, we aimed to identify reliable RGs in the model organism Streptomyces coelicolor. A pool of potential RGs containing 1,471 genes was first identified by determining the intersection of genes with stable transcript levels from four time-series transcriptome microarray datasets of S. coelicolor M145 cultivated in different conditions. Then, following a strict rational selection scheme including homology analysis, disturbance analysis, function analysis and transcript abundance analysis, 13 candidates were selected from the 1,471 genes. Based on real-time quantitative reverse transcription PCR assays, SCO0710, SCO6185, SCO1544, SCO3183 and SCO4758 were identified as the top five genes with the most stable transcript levels among the 13 candidates. Further analyses showed these five genes also maintained stable transcript levels in different S. coelicolor strains, as well as in Streptomyces avermitilis MA-4680 and Streptomyces clavuligerus NRRL 3585, suggesting they could fulfill the requirements of accurate data normalization in streptomycetes. Moreover, the systematic strategy employed in this work could be used for reference in other microorganism to select reliable RGs.